Across a 1000-km stretch of the River Nile, from the 1st Cataract in southern Egypt to the 4th Cataract in Sudan, many hundreds of drystone walls are located within active channels, on seasonally inundated floodplains or in now-dry Holocene palaeochannel belts. These walls (or river groynes) functioned as flood and flow control structures and are of a type now commonly in use worldwide. In the Nile Valley, the structures have been subject only to localised investigations, and none have been radiometrically dated. Some were built within living memory to trap nutrient-rich Nile silts for agriculture, a practice already recorded in the early 19th century C.E. However, others situated within ancient palaeochannel belts indicate construction over much longer time frames. In this paper, we map the distribution of these river groynes using remote sensing and drone survey. We then establish their probable functions and a provisional chronology using ethnoarchaeological investigation and the ground survey, excavation and radiometric dating of the structures in northern Sudan, focusing on the Holocene riverine landscape surrounding the pharaonic settlement of Amara West (c. 1300–1000 B.C.E.). Finally, we consider the historical and economic implications of this form of hydraulic engineering in the Nile Valley over the past three millennia.